estlambda: Estimate the inflation factor for a distribution of P-values

In etnite/bwardr: Brian Ward personal R package

Estimate the inflation factor for a distribution of P-values

Description

NOTE: This is copied (with slight modifications) from the now-defunct GenABEL package. The original 'KS' method has been removed as it had many internal GenABEL dependencies. All credit goes to the function author Yurii Aulchenko.

Usage

estlambda(
  data,
  plot = FALSE,
  proportion = 1,
  method = "regression",
  filter = TRUE,
  df = 1,
  ...
)

Arguments

data	A vector of reals. If all are <=1, it is assumed that this is a vector of P-values, else it is treated as a vector of chi-squares
plot	Whether the plot should be shown or not (default).
proportion	The proportion of lowest P (or chi^2) values to be used when estimating the inflation factor lambda.
method	"regression" (default), "median", or "KS": method to be used for lambda estimation.
filter	if the test statistics with 0-value of chi^2 should be excluded prior to estimation of lambda.
df	Number of degrees of freedom.
...	arguments passed to the plot function.

Details

Estimate the inflation factor for a distribution of P-values or 1df chi-square test. The major use of this procedure is the Genomic Control, but can also be used to visualise the distribution of P-values coming from other tests. Methods implemented include 'median' (median(chi2)/0.455...), regression (of observed onto expected) and 'KS' (optimizing the chi2.1df distribution fit by use of Kolmogorov-Smirnov test)

Value

A list with elements

estimate	Estimate of lambda
se	Standard error of the estimate

Author(s)

Yurii Aulchenko

etnite/bwardr documentation built on Jan. 6, 2023, 7:12 a.m.